The isolation of single types of chromosomes is a critical technology for a wide variety of genome related research projects. The challenge is to recover large numbers of chromosomes with high purity and high molecular weight in a relatively short period of time. Our approach has been to develop an optical sorter for high speed sorting and to adopt commercial sorters (EPICS V and EPICS 752) for conventional chromosome sorting. All three units have dual laser excitation for Chromomycin A3 and Hoechst 33258 bound to the chromosomes. The optical chromosome sorter/selector is capable of sorting rates approximately 30-50 times faster than commercial sorters. With the recent success of cloning very large pieces of DNA (>100 kb) into a variety of large insert cloning vectors, the need for high throughput has become crucial. We have validated the technique of optical sorting (selection) using two different methods of damaging DNA of unwanted chromosomes to a degree that it does not be clone; either by cross-linking or by fragmentation of the DNA to size fragments too small for cloning. Both techniques have been shown to be capable of generating chromosome specific cosmid libraries with greater than 95% purity.